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. 2018 Jun 15;34(12):2158-2160.
doi: 10.1093/bioinformatics/bty055.

AbDesigner3D: a structure-guided tool for peptide-based antibody production

Thammakorn Saethang  1 , Kenneth Hodge  1 , Ingorn Kimkong  2 , D Michael Payne  1 , Mark A Knepper  3 , Trairak Pisitkun  1   3
Affiliations

AbDesigner3D: a structure-guided tool for peptide-based antibody production

Thammakorn Saethang et al. Bioinformatics. .

Abstract

Summary: We present AbDesigner3D, a new tool for identification of optimal immunizing peptides for antibody production using a peptide-based strategy. AbDesigner3D integrates 3D structural data from the Protein Data Bank (PDB) with UniProt data, which includes basic sequence data, post-translational modification sites, SNP occurrences and more. Other features, such as uniqueness and conservation scores, are calculated based on sequences from UniProt. The 3D visualization capabilities allow an intuitive interface, while an abundance of quantitative output simplifies the process of comparing immunogen peptides. Important quantitative features added in this tool include calculation and display of accessible surface area (ASA) and protein-protein interacting residues (PPIR). The specialized data visualization features of AbDesigner3D will greatly assist users to optimize their choice of immunizing peptides.

Availability and implementation: AbDesigner3D is freely available at http://sysbio.chula.ac.th/AbDesigner3D or https://hpcwebapps.cit.nih.gov/AbDesigner3D/.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Two novel outputs in AbDesigner3D, ASA and PPIR (A). User interface of AbDesigner3D (result section) showing panels of interactive heat map (B1), specialized protein structure viewer (B2) and custom options (B3). A residue selected in (B1), as shown in the red rectangle, is highlighted along with its neighboring residues as yellow circles in (B2) (Color version of this figure is available at Bioinformatics online.)
See this image and copyright information in PMC

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